MolNFT v1 · #94390 · protein
Crystal structure of green fluorescent protein LANGFP(BRANCHIOSTOMA lanceolatum)
4HVF · Green fluorescent protein blfp-Y6: “Crystal structure of green fluorescent protein LANGFP(BRANCHIOSTOMA lanceolatum)”. X-ray diffraction, 1 ligand (CR2), 8 pockets (best druggability 0.87). MolNFT v1 #94390 on GenesisL1: 3D…
- PDB
- 4HVF
- Type
- protein
- Length
- 875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green fluorescent protein blfp-Y6
- UniProt
- B1PNB8
- Ligands
- CR2
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Green fluorescent protein blfp-Y6 | protein | 217 | 8% helix, 56% strand | B1PNB8 |
| D | Green fluorescent protein blfp-Y6 | protein | 224 | 9% helix, 54% strand | B1PNB8 |
Ligands and binding sites
- CR2 · {(4Z)-2-(aminomethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.87 | 0.88 | 130 | empty |
| 2 | 54 | 0.73 | 0.99 | 21 | CR2 |
| 3 | 52 | 0.72 | 0.99 | 21 | CR2 |
| 4 | 50 | 0.71 | 0.99 | 23 | CR2 |
| 5 | 52 | 0.71 | 0.98 | 24 | CR2 |
Interfaces
6 interfaces between chains.
- B–D · 1085 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1066 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 968 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 940 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 69 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (chromophore).
Compared structures
- 4HVF · Crystal structure of green fluorescent protein lanGFP(Branchiostoma Lanceolatum) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B1PNB8
- Elsewhere: RCSB PDB 4HVF · PDBe 4HVF · UniProt B1PNB8
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